Unearthing the Soil Microbiome, Climate Change, Carbon Storage Nexus
Soil is one of the most diverse microbial ecosystems in the world, replete with not just bacteria, but fungi, archaea, viruses and protists. These microbial communities are critical to plant health and their resistance to stressors, such as , and even . Soils—and their microbes—provide humans with up to . However, the Food and Agriculture Organization (FAO) predicts that due to human activity and climate change, soil erosion could result in between , depending on the soil. Moreover, new topsoil (the uppermost organic-rich layer of soil, usually the top 5-10 inches) is generated at a sluggish rate of only . As such, soil is also one of Earth's precious non-renewable resources, and its microbial communities sustain that.
The soil and its microbiome are notoriously difficult to generalize because they are so , like moisture, pH, type of vegetation in the area, soil structure and aeration and competition or cooperation with other nearby microbes. Soil health therefore can vary by ecosystem and its local flora and fauna. However, the real business of soils generally occurs in the top layers where organic matter and mineral content are concentrated, and thus life is most amenable to plant roots and microorganisms. Dead vegetation, such as discarded leaves, feeds a carpet of organic decay that replenishes this layer and provides fuel and carbon for the ecosystem below. Good structure in these soil layers allows porous ‘micropockets' to form for water, oxygen and nutrients, making it easier for roots and microbes to weave through.
The Root Microbiome (The ‘Rhizobiome')
The known to man is, incidentally, a single fungus of the honey mushroom family that threads underneath the earthy humus of the mystical Blue Mountains in the Pacific Northwest. Estimated to be between 2,400-8,650 years old, Armillaria ostoyae spreads across more than 2,300 acres of land in what some would call a savory array. Its impressive breadth is a result of seemingly endless networks of hyphae, or microscopic branching filaments, that wend through the rich forest soil.
Although A. ostoyae parasitizes conifer trees (an unfortunate hustle), its way of life doesn't represent soil fungi overall. In fact, an astonishing benefit from symbiosis with fungi, not to mention abundant partnerships with other kingdoms of microbes. Much of this mutualistic exchange is mediated through the plants' roots and the ecological zone surrounding them, dubbed the ‘rhizosphere.'
Plants themselves play no small role in shaping the soil microbiome, as they by luring their . When plants photosynthesize sugars in their leaves, they share some of these sugars—up to —with the below-deck crew via their roots, in what are called ‘exudates' (i.e., secreted by the plant). As plants die off and contribute to leaf litter and organic matter in the topsoil, their unique characteristics also help shape the community of microbes and other creatures that break them down.
Early in a plant's life cycle, it exudes in an effort to recruit cooperative microbes. In response, bacteria and fungi that are able to detect these exudates travel in the direction of the roots and on, around, in between and, in some cases, inside of the roots. In exchange for sugars from the plant, microbes provide the plant with nutrients, water, protection from parasitic organisms and protection from drought. Some mycorrhizal fungi—'myco,' the Latin word for fungus and 'rhiza,' the Greek word for root—can even create a direct connection to the plant roots to facilitate ready nutrient sharing. The spindly (~20x narrower than a human hair), and are able to network into numerous microscopic pockets of nutrients and water in the soil. This network of hyphae helps them scout water that they can then share with the plant and bacterial populations.
Some plants are said to have a stronger "," which is to say that they appear to more selectively recruit the microbes they desire to their root system, whereas others don't seem to recruit as vigorously. They do this by virtue of nuances in their root exudates that even differ by and . The "rhizobiome," as the root microbiome has been called, moves in tandem with the exudates, , including factors such as radial distance extending outward from the root or location on the root itself, in addition to like soil moisture, soil structure and temperature. For these reasons, the rhizobiome can be quite difficult to study.
It's not just the plant that microbes communicate with, but each other. Interkingdom interactions between different members of the rhizobiome are thought to be key in how the whole system functions. For example, fungal mycelia (i.e., the entire network of its hyphae) not only deliver water to isolated bacteria, but between bacteria, serve as and . Protists and nematodes feed on certain populations of bacteria and thus help by predation. Viruses can between microbial groups, such as antimicrobial resistance genes. On a macroscopic level, nematodes and arthropods that burrow through the soil help for water, fungal hyphae and plant roots to intertwine.
Climate Change and Soil Carbon Fixation
In addition to being host to an incredibly important symbiotic exchange between plants and their microbes, soil is also a silo for the majority of carbon found in terrestrial ecosystems (). About half of this terra-carbon is tucked away in the , which are heating up at nearly as other global regions in response to climate change. The soil microbiome and that community's interaction with plants are a central component of the carbon storage process, and . For the arctic, , which decompose organic material and release the large reservoir of into the atmosphere. Forests and grasslands together cover and account for large swaths of carbon soil fixation as well, with grasslands alone making up about 20% of the Earth's soil carbon store.
Climate models have come to differing conclusions about how a warming future could impact soil sequestration or release of carbon, and it likely differs both by regional factors and temporal ones. Some models suggest that higher atmospheric carbon could lead to an initial burst in plant growth and carbon sequestration, but a of soil microbe diversity and activity, and thus a decline in plant viability and back into the atmosphere. However, these models have an intensely intricate number of variables to account for, with little ability to generalize globally.
There are some trends that may indicate how microbes will respond to ongoing climate change. A greater diversity of plants in a region corresponds to more active soil microbes and ; however climate change is slowly of many plant ecosystems. Carbon is also more readily stored in , or else by microbes that can withstand drought stress. However, climate change is ushering forth widespread desertification and , suggesting that fewer soils will be available for adequate carbon fixation unless we can develop and support microbial solutions.
According to field studies, elevated carbon in the atmosphere is able to of multiple microbial kingdoms, including fungi, archaea and bacteria. Functional studies indicate in these populations that genes involved in different aspects of were enriched in surviving communities, which could imply that rhizobiome shifts favor those microbes that can keep up with emerging metabolic demands. Atmospheric warming, independent of atmospheric carbon, has a documented effect on the of the microbial community as well. In general, fungi are less heat-resistant than bacteria, and warming can increase the bacteria:fungal ratio. Recall that fungi are important shuttles of nutrients and water due to their narrow branching mycelia, thus their loss can have detrimental impacts on other interkingdom communities and on the plants they partner with.
Climate change is also affiliated with more , such as drought, flooding and irregular seasons. These fluctuations in soil moisture, , can have deleterious effects on its microbiome and carbon sequestration. Studies indicate that while soil communities can demonstrate resilience to an initial dry/wetting cycle, . On the brighter side, bacterial communities on roots can , and are currently an intervention under investigation.
Climate-Friendly Soil Interventions
Some work has been done investigating the use of microbial interventions to regenerate soil or provide enhanced resilience to plants. Making use of the natural ability of some microbes to sequester carbon, much research is underway to investigate in balancing the carbon ledger. Strategies abound, from using autotrophic organisms like algae to , to to improve carbon sequestration efficiency, to in bacteria, to direct .
Other approaches have focused on the relationship between plants and their rhizobiome, working to increase plant resilience through microbial supplementation. When applied to soil, for instance, some fungi can help plants , which is important in a time of increasing aridification. Bacterial treatments were also able to by reducing reactive oxygen species, and also . and has been shown to boost plant health.
Microbes have also been investigated for bioremediation efforts, such as the conversion of , into stable and less harmful forms. This enhances the safety of agricultural production and helps restore polluted agricultural land.
As creative and emergent as these solutions are, the still accounts for the lion's share of greenhouse gas emissions. Soils, their plants and their microbiomes—the foundation of food production—will continue to suffer from elevated temperatures and atmospheric carbon until these factors can be brought under control.
How can microbial culture collections be used to infer ecological and evolutionary responses to warming soil temperature? Find out in this episode of "Meet the Microbiologist" featuring Dr. Mallory Choudoir.
